Merge pull request #127 from KVSlab/refactor-aneu-tools

Rename ToolRepairSTL

src/vampy/__init__.py

@@ -12,7 +12,7 @@
  from .automatedPreprocessing import DisplayData
  from .automatedPreprocessing import ImportData
  from .automatedPreprocessing import NetworkBoundaryConditions
- from .automatedPreprocessing import ToolRepairSTL
+ from .automatedPreprocessing import repair_tools
  from .automatedPreprocessing import automated_preprocessing
  from .automatedPreprocessing import preprocessing_common
  from .automatedPreprocessing import simulate
@@ -55,7 +55,7 @@
  "ImportData",
  "NetworkBoundaryConditions",
  "simulate",
- "ToolRepairSTL",
+ "repair_tools",
  "visualize",
  "vmtk_pointselector",
  "Artery",

src/vampy/automatedPreprocessing/__init__.py

@@ -4,6 +4,6 @@
 from . import ImportData
 from . import NetworkBoundaryConditions
 from . import simulate
-from . import ToolRepairSTL
+from . import repair_tools
 from . import visualize
 from . import vmtk_pointselector

src/vampy/automatedPreprocessing/automated_preprocessing.py

@@ -10,12 +10,12 @@
  prepare_output_surface, vmtk_compute_geometric_features
 
 # Local imports
-from vampy.automatedPreprocessing import ToolRepairSTL
 from vampy.automatedPreprocessing.moving_common import get_point_map, project_displacement, save_displacement
 from vampy.automatedPreprocessing.preprocessing_common import read_polydata, get_centers_for_meshing, \
  dist_sphere_diam, dist_sphere_curvature, dist_sphere_constant, get_regions_to_refine, add_flow_extension, \
  write_mesh, mesh_alternative, generate_mesh, find_boundaries, compute_flow_rate, setup_model_network, \
  radiusArrayName, scale_surface, get_furtest_surface_point, check_if_closed_surface, remesh_surface
+from vampy.automatedPreprocessing.repair_tools import find_and_delete_nan_triangles, clean_surface, print_surface_info
 from vampy.automatedPreprocessing.simulate import run_simulation
 from vampy.automatedPreprocessing.visualize import visualize_model
 
@@ -121,10 +121,10 @@ def run_pre_processing(input_model, verbose_print, smoothing_method, smoothing_f
  surface = vtk_triangulate_surface(surface)
 
  # Check the mesh if there is redundant nodes or NaN triangles.
- ToolRepairSTL.surfaceOverview(surface)
- ToolRepairSTL.foundAndDeleteNaNTriangles(surface)
- surface = ToolRepairSTL.cleanTheSurface(surface)
- foundNaN = ToolRepairSTL.foundAndDeleteNaNTriangles(surface)
+ print_surface_info(surface)
+ find_and_delete_nan_triangles(surface)
+ surface = clean_surface(surface)
+ foundNaN = find_and_delete_nan_triangles(surface)
  if foundNaN:
  raise RuntimeError(("There is an issue with the surface. "
  "Nan coordinates or some other shenanigans."))

src/vampy/automatedPreprocessing/repair_tools.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+
+# Program: AneuTool
+# Module: ToolRepairSTL.py
+# Language: Python
+# Date: $Date: 2016/17/04 00:00:00 $
+# Version: $Revision: 0.0.1 $
+# Author: Christophe Chnafa
+
+# Copyright (c) Christophe Chnafa. All rights reserved.
+
+import vtk
+
+
+def is_nan(num):
+ return num != num
+
+
+def print_surface_info(surface):
+ nTriangles = surface.GetNumberOfCells()
+ nPoints = surface.GetNumberOfPoints()
+ print("> --- Surface overview:")
+ print(("> Total number of triangles: %s." % nTriangles))
+ print(("> Total number of points: %s." % nPoints))
+ print(">")
+
+
+def find_and_delete_nan_triangles(surface):
+ ctrNaN = 0
+ foundNaN = False
+ nTriangles = surface.GetNumberOfCells()
+ print("> --- Check the surface.")
+ # The links from points to cells need to be build.
+ surface.BuildLinks()
+ for i in range(0, nTriangles):
+ killThisTriangle = False
+ nPointsForThisCell = surface.GetCell(i).GetPoints().GetNumberOfPoints()
+ if nPointsForThisCell > 3:
+ print("> WARNING: found Cell with more than 3 points: there is more than triangles.")
+ for j in range(0, nPointsForThisCell):
+ x = [0.0, 0.0, 0.0]
+ surface.GetCell(i).GetPoints().GetPoint(j, x)
+ if is_nan(x[0]) | is_nan(x[1]) | is_nan(x[2]):
+ ctrNaN += 1
+ killThisTriangle = True
+ if killThisTriangle:
+ surface.DeleteCell(i)
+ surface.RemoveDeletedCells()
+ print(("> Found %s NaN cells." % ctrNaN))
+ print(">")
+ if ctrNaN > 0:
+ foundNaN = True
+
+ return foundNaN
+
+
+def clean_surface(surface):
+ print("> --- Cleaning the surface.")
+ cleanPolyData = vtk.vtkCleanPolyData()
+ if vtk.VTK_MAJOR_VERSION <= 5:
+ cleanPolyData.SetInput(surface)
+ else:
+ cleanPolyData.SetInputData(surface)
+ cleanPolyData.PointMergingOff() # point locator will not be used, and points
+ # that are not used by any cells will be eliminated,
+ # but never merged.
+
+ # In VTK the tolerance is defined as a fraction
+ # of the bounding box length.
+ tol = 0.0 # 0.0005
+ cleanPolyData.SetTolerance(tol)
+ cleanPolyData.Update()
+
+ cleanPolyData.Update()
+ outputPolyData = cleanPolyData.GetOutput()
+
+ print("> Done.")
+ print("> ")
+
+ return (outputPolyData)